rs12587781

Variant names:

• chr14-22530666-G-T
• rs12587781

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.835 in 152,142 control chromosomes in the GnomAD database, including 53,862 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.83 (53862 hom., cov: 31)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 9 publications found

Genes affected

TRA (HGNC:12027):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126889 AN: 152022 Hom.: 53801 Cov.: 31

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.851

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.835 AC: 127007 AN: 152142 Hom.: 53862 Cov.: 31 AF XY: 0.826 AC XY: 61431 AN XY: 74416

African (AFR) AF: 0.903 AC: 37470 AN: 41510

American (AMR) AF: 0.802 AC: 12266 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2954 AN: 3470

East Asian (EAS) AF: 0.344 AC: 1783 AN: 5178

South Asian (SAS) AF: 0.705 AC: 3388 AN: 4808

European-Finnish (FIN) AF: 0.788 AC: 8325 AN: 10562

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57903 AN: 68000

Other (OTH) AF: 0.852 AC: 1802 AN: 2116

Alfa AF: 0.842 Hom.: 90954

Bravo AF: 0.837

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.33
PhyloP100		-1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12587781; hg19: chr14-22999617;